Excerpt
This page describes how to run JupyterLab in a container on Pawsey systems with Slurm. This involves launching JupyterLab and then connecting to the Jupyter server.

...

For this example, we're going to be using the jupyter/datascience-notebook (external site) Docker image. It provides a Conda environment with a large collection of common Python packages (including NumPy, SciPy, Pandas, Scikit-learn, Bokeh and Matplotlib), an R environment (with the tidyverse (external site) packages), and a Julia environment. All of these are accessible via a Jupyter notebook server.

This Docker image ships with a startup script that allows for a number of runtime options to be specified. Most of these are specific to running a container using Docker; we will focus on how to run this container using Singularity.

The datascience-notebook image has a default user, jovyan, and it assumes that you will be able to write to /home/jovyan. When you run a Docker container via Singularity, you will be running as your Pawsey username inside the container, so we won't be able to write to /home/jovyan. Instead, we can mount a specific directory (on Pawsey's filesystems) into the container at /home/jovyan. This will allow our Jupyter server to do things like save notebooks and write checkpoint files, and those will persist on Pawsey's filesystem after the container has stopped.

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The following script launches a Jupyter notebook on a compute node (download the template batch script). The first step is to enter a writable directory with some space, such as /scratch, to launch the notebook. Create a directory where you will start our Jupyter notebook container and put any relevant data or Jupyter notebooks in this directory. This is also the directory that will be mounted to /home/jovyan.

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Code Block

language	bash
theme	Emacs
title	Listing 1. Slurm script for running JupyterHub in a GPU-enabled container
collapse	true

#!/bin/bash -l
# Allocate slurm resources, edit as necessary
#SBATCH --account=[your-project-name]
# Here we request the appropriate partition for the system
#SBATCH --partition=work
# Since jupyterlab is not mpi enabled, we just use one task 
#SBATCH --ntasks=1
#SBATCH --mem=20GB
#SBATCH --time=02:00:00
#SBATCH --job-name=jupyter_notebook
#SBATCH --export=NONE

# Set our working directory
# This is the directory we'll mount to /home/jovyan in the container
# Should be in a writable path with some space, like /scratch
jupyterDir="${MYSCRATCH}/jupyter-dir"

# Set the image and tag we want to use
image="docker://jupyter/datascience-notebook:latest"

# You should not need to edit the lines below

# Prepare the working directory
mkdir -p ${jupyterDir}
cd ${jupyterDir}

# Get the image filename
imagename=${image##*/}
imagename=${imagename/:/_}.sif

# Get the hostname 
# We'll set up an SSH tunnel to connect to the Juypter notebook server
host=$(hostname)

# Set the port for the SSH tunnel
# This part of the script uses a loop to search for available ports on the node;
# this will allow multiple instances of GUI servers to be run from the same host node
port="8888"
pfound="0"
while [ $port -lt 65535 ] ; do
  check=$( ss -tuna | awk '{print $4}' | grep ":$port *" )
  if [ "$check" == "" ] ; then
    pfound="1"
    break
  fi
  : $((++port))
done
if [ $pfound -eq 0 ] ; then
  echo "No available communication port found to establish the SSH tunnel."
  echo "Try again later. Exiting."
  exit
else
  echo "Port to use is port=${port}"
fi

# Load Singularity
module load singularity/34.111.40-nompi
:0
# Pull our image in a folder
singularity pull $imagename $image

echo "*****************************************************"
echo "Setup - from your laptop do:"
echo "ssh -N -f -L ${port}:${host}:${port} $USER@$PAWSEY_CLUSTER.pawsey.org.au"
echo "*****"
echo "The launch directory is: $jupyterDir"
echo "*****************************************************"
echo ""
echo "*****************************************************"
echo "Terminate - from your laptop do:"
echo "kill \$( ps x | grep 'ssh.*-L *${port}:${host}:${port}' | awk '{print \$1}' )"
echo "*****************************************************"
echo ""
 
# Launch our container
# and mount our working directory to /home/jovyan in the container
# and bind the run time directory to our home directory
singularity exec -C \
  -B ${jupyterDir}:/home/joyvan \
  -B ${jupyterDir}:${HOME} \
  ${imagename} \
  jupyter notebook \
  --no-browser \
  --port=${port} --ip=0.0.0.0 \
  --notebook-dir=${jupyterDir}

...

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width	900px

Code Block

language	bash
theme	DJango
title	Terminal 1. Launching JupyterHub and extracting connection information
collapse	true

$ sbatch jupyter-notebook-one-singularity.slm
Submitted batch job 3528476
$ cat slurm-3528476.out
.
.
.
Writing manifest to image destination
Storing signatures
[34mINFO:   [0m Creating SIF file...
[34mINFO:   [0m Build complete: /scratch/pawsey0002pawsey12345/matilda/jupyter-dir/singularity-cache/cache/oci-tmp/18ef2702c6a25bd26b81e7b6dc831adb2bc294ae7bc9b011150b8f4573c41d4a/datascience-notebook_latest.sif

*****************************************************
Setup - from your laptop do:
ssh -N -f -L 8888:z123nid001007:8888 <user>@setonix.pawsey.org.au
*****
The launch directory is: /scratch/pawsey0001/...
*****************************************************

*****************************************************
Terminate - from your laptop do:
kill $( ps x | grep 'ssh.*-L *8888:z123nid001007:8888' | awk '{print $1}' )
*****************************************************

[I 04:38:34.503 NotebookApp] Writing notebook server cookie secret to /home/matilda/.local/share/jupyter/runtime/notebook_cookie_secret
[I 04:38:36.677 NotebookApp] JupyterLab extension loaded from /opt/conda/lib/python3.7/site-packages/jupyterlab
[I 04:38:36.677 NotebookApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
[I 04:38:37.605 NotebookApp] Serving notebooks from local directory: /group/pawsey0002pawsey12345/matilda/jupyter-dir
[I 04:38:37.605 NotebookApp] The Jupyter Notebook is running at:
[I 04:38:37.605 NotebookApp] http://z123nid001007:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242
[I 04:38:37.605 NotebookApp]  or http://127.0.0.1:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242
[I 04:38:37.605 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 04:38:37.616 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///home/matilda/.local/share/jupyter/runtime/nbserver-17-open.html
    Or copy and paste one of these URLs:
        http://z123nid001007:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242
     or http://127.0.0.1:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242

In a separate local terminal window, run SSH based on the command listed in the output file. Look for the section that says "Setup - from your laptop do" and, from your laptop, type the command. In this example this would be:

ssh -N -f -L 8888:z123nid001007:8888 <username>@setonix.pawsey.org.au

After this step, you can open up a web browser and use copy-paste the address displayed in the output file to access your Jupyter notebook. Look for the section that says "To access the notebook, ...", and copy-paste the address in your web browser. In this example the address isto copy-paste is:

http://127.0.0.1:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242

...

Column

Figure 1. Jupyter authentication page

Note

title	Note:

The information above is a notebook launched on zeussetonix.pawsey.org.au. Ensure that you look at your output to select the correct machine.

Clean up when you are finished

Once you have finished:

Cancel your job with scancel.
Kill the SSH tunnel, based on the command displayed in the output file:

kill $( ps x | grep 'ssh.*-L *8888:z123:8888' | awk '{print $1}' )

Run a GPU-enabled Jupyter notebook

Warning

title	This section is being updated for AMD GPUs

This section about the use of Jupiter notebooks with GPUs is currently being updated to work with AMD GPUs on Setonix. The existing information at this point in time is not accurate and should not be considered as useful until this warning is removed.

Running a GPU-enabled container on GPU Pawsey systems with Slurm is very similar to running a standard Jupyter notebook. The main differences are:

Use of the gpu partition on Setonix
Request a GPU to Slurm
Pass the environment variable CUDA_HOME to Singularity
Run the container using the flag --nv, to enable the GPU support from Singularity

...

width	900px

Code Block

language	bash
theme	Emacs
title	Listing 2. Slurm script for running JupyterHub in a GPU-enabled container
collapse	true

#!/bin/bash -l
# This example is for GPUs on Setonix
# Allocate slurm resources, edit as necessary
#SBATCH --account=[your-project-name]
# Here we request the appropriate GPU partition on a system
#SBATCH --partition=gpu
# Be aware that the request for GPU resources may change in later versions of slurm
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --time=02:00:00
#SBATCH --job-name=jupyter_notebook
#SBATCH --export=NONE

# Set our working directory
# This is the directory we'll mount to /home/jovyan in the container
# Should be in a writable path with some space, like /scratch
jupyterDir="${MYSCRATCH}/jupyter-dir"

# Set the image and tag we want to use
image="docker://jupyter/datascience-notebook:latest"

# You should not need to edit the lines below

# Prepare the working directory
mkdir -p ${jupyterDir}
cd ${jupyterDir}

# Get the image filename
imagename=${image##*/}
imagename=${imagename/:/_}.sif

# Get the hostname
# We'll set up an SSH tunnel to connect to the Juypter notebook server
host=$(hostname)

# Set the port for the SSH tunnel
# This part of the script uses a loop to search for available ports on the node;
# this will allow multiple instances of GUI servers to be run from the same host node
port="8888"
pfound="0"
while [ $port -lt 65535 ] ; do
  check=$( ss -tuna | awk '{print $4}' | grep ":$port *" )
  if [ "$check" == "" ] ; then
    pfound="1"
    break
  fi
  : $((++port))
done
if [ $pfound -eq 0 ] ; then
  echo "No available communication port found to establish the SSH tunnel."
  echo "Try again later. Exiting."
  exit
fi

# Load Singularity
module load singularity/3.11.4-nompi

# Load ROCm and set environment variable for Singularity
module load rocm/5.2.3
export SINGULARITYENV_CUDA_HOME=$CUDA_HOME

# Pull our image in a folder
singularity pull $imagename $image

echo "*****************************************************"
echo "Setup - from your laptop do:"
echo "ssh -N -f -L ${port}:${host}:${port} $USER@$PAWSEY_CLUSTER.pawsey.org.au"
echo "*****"
echo "The launch directory is: $jupyterDir"
echo "*****************************************************"
echo ""
echo "*****************************************************"
echo "Terminate - from your laptop do:"
echo "kill \$( ps x | grep 'ssh.*-L *${port}:${host}:${port}' | awk '{print \$1}' )"
echo "*****************************************************"
echo ""
 
# Launch our container
# and mount our working directory to /home/jovyan in the container
# and bind the run time directory to our home directory
singularity exec --nv -C \
  -B ${jupyterDir}:/home/joyvan \
  -B ${jupyterDir}:$HOME \
  ${imagename} \
  jupyter notebook \
  --no-browser \
  --port=${port} --ip=0.0.0.0 \
  --notebook-dir=${jupyterDir}

Testing your notebook with a simple example GPU code

Try copying and pasting the following snippet inside a Jupyter cell. This python code uses the numba python library to run some calculations with a Nvidia GPU.

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width	900px

Code Block

language	py
theme	Emacs
title	Listing 3. Simple GPU-enabled Python code snippet
collapse	true

# key GPU library from numba import cuda import numpy as np # define some kernels @cuda.jit def add_kernel(x, y, out): idx = cuda.grid(1) out[idx] = x[idx] + y[idx] n = 4096 x = np.arange(n).astype(np.int32) # [0...4095] on the host y = np.ones_like(x) # [1...1] on the host out = np.zeros_like(x) # cuda commands to copy memory to the device d_x = cuda.to_device(x) d_y = cuda.to_device(y) d_out = cuda.to_device(out) # run kernel threads_per_block = 128 blocks_per_grid = 32 add_kernel[blocks_per_grid, threads_per_block](d_x, d_y, d_out) cuda.synchronize() # output result print(d_out.copy_to_host()) # Should be [1...4096]

Also note that the available version of the singularity module in the system may have changed, so that you need to adapt the script accordingly.

From the Jupyter notebook menu, you can create a new notebook and start from there. If you already count with a notebook that you want to execute/develop, you may need to copy it into the jupiter-dir first.

Clean up when you are finished

Once you have finished (and saved and exited from the Jupyter notebook instance):

From the Pawsey cluster, cancel your job with scancel.
From your own computer, kill the SSH tunnel, based on the command displayed in the output file. Look for the section that says "Terminate - from your laptop do" and execute the command from your laptop. In this example, you should type:

kill $( ps x | grep 'ssh.*-L *8888:nid001007:8888' | awk '{print $1}' )

External links

DockerHub
For information about runtime options supported by the startup script in the Jupyter image, see Common Features in the Jupyter Docker Stacks documentation
The Rocker Project ("Docker Containers for the R Environment")

Versions Compared

Old Version 10

New Version Current

Key

Clean up when you are finished

Run a GPU-enabled Jupyter notebook

Testing your notebook with a simple example GPU code

Clean up when you are finished

External links

Page Comparison

Versions Compared

Old Version 10

New Version Current

Key

Clean up when you are finished

Run a GPU-enabled Jupyter notebook

Testing your notebook with a simple example GPU code

Clean up when you are finished

External links